Identification of key genes and the pathophysiology associated with allergen-specific immunotherapy for allergic rhinitis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37430199", "kind": "science-record", "revision": 5, "content_hash": "sha256:ef47d071b2e2de89eeeccedc19b4b2398c1c402aff70871fbfe6615a827fed8d", "created_at": "2026-11-01T19:02:11Z", "updated_at": "2026-11-01T22:52:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes and the pathophysiology associated with allergen-specific immunotherapy for allergic rhinitis.", "doi": "10.1186/s12865-023-00556-1", "pmid": "37430199", "authors": ["Kai Fan", "Shican Zhou", "Ling Jin", "Shiwang Tan", "Ju Lai", "Zimu Zhang", "Jingwen Li", "Xiayue Xu", "Chunyan Yao", "Zhiqiang Yan", "Shaoqing Yu"], "journal": "BMC immunology", "year": 2023, "abstract": "BACKGROUND: Allergen-specific immunotherapy (AIT) is a causative treatment in allergic rhinitis (AR), comprising long-term allergen administration and over three years of treatment. This study is carried out for revealing the mechanisms and key genes of AIT in AR.\nMETHODS: The present study utilized online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE37157 and GSE29521 to analyze the hub genes changes related to AIT in AR. Based on limma package, differential expression analysis for the two groups (samples of allergic patients prior to AIT and samples of allergic patients undergoing AIT) was performed to obtain differentially expressed genes (DEGs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs were conducted using DAVID database. A Protein-Protein Interaction network (PPI) was built and a significant network module was acquired by using Cytoscape software (Cytoscape, 3.7.2). Utilizing the miRWalk database, we identified potential gene biomarkers, constructed interaction networks of target genes and microRNAs (miRNAs) using Cytoscape software, and explore the cell type-specific expression patterns of these genes in peripheral blood using publicly available single-cell RNA sequencing data (GSE200107). Finally, we are using PCR to detect changes in the hub genes that are screened using the above method in peripheral blood before and after AIT treatment.\nRESULTS: GSE37157 and GSE29521 included 28 and 13 samples, respectively. A total of 119 significantly co-upregulated DEGs and 33 co-downregulated DEGs were obtained from two datasets. The GO and KEGG analyses demonstrated that protein transport, positive regulation of apoptotic process, Natural killer cell mediated cytotoxicity, T cell receptor signaling pathway, TNF signaling pathway, B cell receptor signaling pathway and Apoptosis may be potential candidate therapeutic targets for AIT of AR. From the PPI network, 20 hub genes were obtained. Among them, the PPI sub-networks of CASP3, FOXO3, PIK3R1, PIK3R3, ATF4, and POLD3 screened out from our study have been identified as reliable predictors of AIT in AR, especially the PIK3R1.\nCONCLUSION: Our analysis has identified novel gene signatures, thereby contributing to a more comprehensive understanding of the molecular mechanisms underlying AIT in the treatment of AR.", "claims": [{"id": "claim-method", "statement": "In this study, we performed the online analytical tool GEO2R for differential expression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37430199", "locator": "sections[13] \"Data processing and identification of DEGs\" paragraph 2", "quote": "In this study, we performed the online analytical tool GEO2R for differential expression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated for this study can be found in the Gene Expression Omnibus database (GEO, www.ncbi.nlm.nih.gov/geo/):GSE37157, GSE29521 and GSE200107.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37430199", "locator": "sections[24] \"notes\" paragraph 1", "quote": "The datasets generated for this study can be found in the Gene Expression Omnibus database (GEO, www.ncbi.nlm.nih.gov/geo/):GSE37157, GSE29521 and GSE200107."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After removing duplicate genes and expression values lacking specific gene symbols, we obtained 119 jointly up-regulated DEGs and 33 jointly down-regulated DEGs from the two datasets (P value < 0.05 and |logFC|> 0.5) (Fig. 1C, D).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "After removing duplicate genes and expression values lacking specific gene symbols, we obtained 119 jointly up-regulated DEGs and 33 jointly down-regulated DEGs from the two datasets (P value < 0.05 and |logFC|> 0.5) (Fig. 1C, D)."}, "evidence": [{"asset": "source:pmid:37430199", "locator": "sections[3] \"Identification of differentially expressed genes\" paragraph 2", "quote": "After removing duplicate genes and expression values lacking specific gene symbols, we obtained 119 jointly up-regulated DEGs and 33 jointly down-regulated DEGs from the two datasets (P value < 0.05 and |logFC|> 0.5) (Fig. 1C, D)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "After removing duplicate genes and expression values lacking specific gene symbols, we obtained 119 jointly up-regulated DEGs and 33 jointly down-regulated DEGs from the two datasets (P value < 0.05 and |logFC|> 0.5) (Fig. 1C, D).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37430199"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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